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or if you insist on working with ls -lt, the old awk/cut trick:
ls -lt | awk '{print $NF, $0}' | sort -t '.' -k1,1 -k2.2,2n | cut -d ' ' -f2-

It becomes simpler when you only have the file names, i.e. with a simple ls command.
Then you can use the dot as the field delimiter, sort for field #1 primary and field #2 secondary. And in field...